From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jan 30 2004 - 10:43:36 CST
Hello Frances,
First of all, just narrow things down to one segment and solve the
problems there.
Second, the warnings below may be okay if that residue is at one of the
terminii of the peptide. you can't generate complete dihedrals or
improper torsions for residues at the ends of a peptide chain.
Third, it seems from the log file that large chunks of residues are
missing within segment 1 and others. This is not helpful. Find out why
they are missing and then proceed to the next segment. If you have to make
more segments so be it. psfgen is trying to create bonds between residues
that are missing within a segment and that is truly not helpful.
Fourth, if you visualize the pdb file in VMD, look for cysteine residues
closer than 8A. If the structure is from the pdbdatabank, disulfides
should be listed. Having said this, I doubt disulfides are the problem
here.
Brian
On Fri, 30 Jan 2004, Frances Leung wrote:
> Hi,
>
> It may have to do with the missing residues in the protein? When I was
> generating the psf file using psfgen, I got warnings like:
>
> extracted 26 residues from pdb file
> generating structure at end of segment
> no residue 1 before GLU:698 of segment SEG0
> Warning: add improper failed in residue GLU:698
> no residue 1 before GLU:698 of segment SEG0
> Warning: add conformation C-N-CA-C failed in residue GLU:698
> no residue 1 before GLU:698 of segment SEG0
> Warning: add conformation C-CA-N-HN failed in residue GLU:698
> .....
> the log file is attached.
>
> what should I do to get rid of these warnings? Do I need to use the
> patch command, I don't think there are disulfide bonds in the protein
> however. If there are, how can I find out?
>
> Frances
>
> -----Original Message-----
> From: Harindar Keer [mailto:hkeer_at_uci.edu]
> Sent: Thursday, January 29, 2004 4:21 PM
> To: Frances Leung
> Cc: namd-l_at_ks.uiuc.edu
> Subject: RE: namd-l: minimization problem - "Bad global exclusion
> count,possible error!"
>
> Hi,
>
> Check if some bonds in complex are crossing the periodic cell
> boundary, fixing the complex such that nothing crosses the boundary
> before minimization might help. Although I am not sure but reason might
> lie in way interactions are calculated under boundary conditions, as one
> atom leaves one side of cell it appears in the cell from opposite side.
> Being part of same bond but now more than cutoff distance away might
> cause the warning.
> Please correct if someone knows the reason.
>
> Regards,
>
>
> On Thu, 2004-01-29 at 19:20, Frances Leung wrote:
> > Hello,
> >
> > I think it's a little different for my case. Previously I
> successfully
> > minimized my protein complex. I even finished equilibrating it.
> > However, the process took so long and I expected the SMD would take
> even
> > longer and due to time constraints, I decided to do just half of the
> > protein (the protein has two chains, now I'm trying to do simulation
> on
> > just one of the chains to save time since both chains are essentially
> > identical). I didn't get warnings like these when I was minimizing
> the
> > complete protein complex, but now that I'm doing just half of it, I
> get
> > problems. I wonder what I need to do to get through the minimization
> > part by simulating just one chain?
> >
> > Frances
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> > Behalf Of Brian Bennion
> > Sent: Thursday, January 29, 2004 3:47 PM
> > To: Uday Chippada
> > Cc: namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: minimization problem - "Bad global exclusion
> count,
> > possible error!"
> >
> > Hello,
> >
> > After having a problem in my topology file cause the same error I
> would
> > highly advise looking at the HYP residue you created and make sure the
> > bonding is corect. Just checking the psf file in vmd didn't catch my
> > mistake. It sounds like a bond is actually missing in your case.
> >
> > Regards,
> > Brian
> >
> >
> > On Thu, 29 Jan 2004, Uday Chippada wrote:
> >
> > > Hi,
> > >
> > > I am getting the same error too. Also in the end the error that is
> > > shown is something like
> > >
> > > ERROR: Constraint failure in RATTLE algorithm for atom 231!
> > > ERROR: Constraint failure; simulation has become unstable.
> > > ERROR: Exiting prematurely.
> > >
> > > I recieved the same error while working with the 1QSU molecule which
> > > had a HYP residue, for which there was no entries in topology file
> or
> > > the parameter file. So I included these values for HYP, and got the
> > > error. So I attributed it to the HYP residue.
> > >
> > > But when I tried for the 1A3J chain from the protein data bank, I
> > still
> > > got the same error, this one has just PRO and GLY residues.
> > >
> > > I read in some previous messages that it could be because of the
> > sphere
> > > radius, but I checked it and even varied it drastically to no avail.
> > >
> > > When I try the 1UBQ given in the tutorial on the NAMD site, it works
> > > fine.
> > >
> > > Any help would be greatly appreciated. Thank you
> > > Sincerely
> > > Uday Chippada.
> > >
> > > > Hi,
> > > >
> > > > I'm trying to do the minimization for a protein complex and keep
> > > getting
> > > > these warnings:
> > > >
> > > > Warning: Bad global exclusion count, possible error!
> > > > Warning: Increasing cutoff during minimization may avoid this.
> > > >
> > > > Does anyone know what this means? The log file is attached.
> > > >
> > > > Regards,
> > > >
> > > > Frances
> > > >
> > >
> > >
> > >
> >
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
>
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
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